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- PDB-1h9d: Aml1/cbf-beta/dna complex -

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Basic information

Entry
Database: PDB / ID: 1h9d
TitleAml1/cbf-beta/dna complex
Components
  • CORE-BINDING FACTOR ALPHA SUBUNIT1
  • CORE-BINDING FACTOR CBF-BETA
  • DNA (5'-(*CP*AP*AP*CP*CP*GP*CP*AP*AP*C)-3')
  • DNA (5'-(*GP*TP*TP*GP*CP*GP*GP*TP*TP*G)-3')
KeywordsTRANSCRIPTION FACTOR
Function / homology
Function and homology information


regulation of connective tissue replacement / peripheral nervous system neuron development / positive regulation of granulocyte differentiation / RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / Organic cation transport / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions ...regulation of connective tissue replacement / peripheral nervous system neuron development / positive regulation of granulocyte differentiation / RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / Organic cation transport / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation / regulation of cardiac muscle cell proliferation / cardiac muscle tissue regeneration / myeloid leukocyte differentiation / negative regulation of CD4-positive, alpha-beta T cell differentiation / negative regulation of granulocyte differentiation / lymphocyte differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / positive regulation of extracellular matrix organization / RUNX2 regulates genes involved in cell migration / RUNX2 regulates genes involved in differentiation of myeloid cells / Transcriptional regulation by RUNX2 / regulation of plasminogen activation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / myeloid cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / definitive hemopoiesis / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of RUNX1 Expression and Activity / hematopoietic stem cell proliferation / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of cell differentiation / RUNX2 regulates osteoblast differentiation / RUNX3 regulates p14-ARF / hemopoiesis / positive regulation of collagen biosynthetic process / chondrocyte differentiation / cell maturation / positive regulation of interleukin-2 production / ossification / transcription corepressor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Regulation of RUNX3 expression and activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / transcription coactivator binding / neuron differentiation / osteoblast differentiation / Pre-NOTCH Transcription and Translation / protein polyubiquitination / Transcriptional regulation of granulopoiesis / Regulation of RUNX2 expression and activity / positive regulation of angiogenesis / SARS-CoV-1 activates/modulates innate immune responses / RUNX1 regulates transcription of genes involved in differentiation of HSCs / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription by RNA polymerase II / transcription coactivator activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / intracellular membrane-bounded organelle / calcium ion binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / membrane / nucleus
Similarity search - Function
Polyomavirus Enhancer Binding Protein 2; Chain: A; / Core binding factor, beta subunit / Runx, central domain superfamily / Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain / Runx inhibition domain / Runt domain profile. ...Polyomavirus Enhancer Binding Protein 2; Chain: A; / Core binding factor, beta subunit / Runx, central domain superfamily / Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain / Runx inhibition domain / Runt domain profile. / Core-binding factor, beta subunit / Core-binding factor, beta subunit superfamily / Core binding factor beta subunit / Immunoglobulin-like - #720 / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / Runt-related transcription factor 1 / Core-binding factor subunit beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBravo, J. / Warren, A.J.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: The Leukemia-Associated Aml1 (Runx1)-Cbfbeta Complex Functions as a DNA-Induced Molecular Clamp
Authors: Bravo, J. / Li, Z. / Speck, N.A. / Warren, A.J.
History
DepositionMar 7, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_residues
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CORE-BINDING FACTOR ALPHA SUBUNIT1
B: CORE-BINDING FACTOR CBF-BETA
C: CORE-BINDING FACTOR ALPHA SUBUNIT1
D: CORE-BINDING FACTOR CBF-BETA
E: DNA (5'-(*GP*TP*TP*GP*CP*GP*GP*TP*TP*G)-3')
F: DNA (5'-(*CP*AP*AP*CP*CP*GP*CP*AP*AP*C)-3')
G: DNA (5'-(*GP*TP*TP*GP*CP*GP*GP*TP*TP*G)-3')
H: DNA (5'-(*CP*AP*AP*CP*CP*GP*CP*AP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)73,6308
Polymers73,6308
Non-polymers00
Water1,00956
1
A: CORE-BINDING FACTOR ALPHA SUBUNIT1
B: CORE-BINDING FACTOR CBF-BETA
E: DNA (5'-(*GP*TP*TP*GP*CP*GP*GP*TP*TP*G)-3')
F: DNA (5'-(*CP*AP*AP*CP*CP*GP*CP*AP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)36,8154
Polymers36,8154
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-6 kcal/mol
Surface area18270 Å2
MethodPQS
2
C: CORE-BINDING FACTOR ALPHA SUBUNIT1
D: CORE-BINDING FACTOR CBF-BETA
G: DNA (5'-(*GP*TP*TP*GP*CP*GP*GP*TP*TP*G)-3')
H: DNA (5'-(*CP*AP*AP*CP*CP*GP*CP*AP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)36,8154
Polymers36,8154
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-9.5 kcal/mol
Surface area18390 Å2
MethodPQS
Unit cell
Length a, b, c (Å)115.033, 115.033, 133.925
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CORE-BINDING FACTOR ALPHA SUBUNIT1 / CBFA2/PEPBP2AB/RUNX1 / AML-1


Mass: 14909.090 Da / Num. of mol.: 2 / Fragment: RUNT DOMAIN RESIDUES 50-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: AML1 / Plasmid: PRSET / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q01196
#2: Protein CORE-BINDING FACTOR CBF-BETA


Mass: 15815.746 Da / Num. of mol.: 2 / Fragment: HETERODIMERISATION DOMAIN RESIDUES 2-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: CBFB / Plasmid: PRSET / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q13951
#3: DNA chain DNA (5'-(*GP*TP*TP*GP*CP*GP*GP*TP*TP*G)-3')


Mass: 3107.025 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: DNA chain DNA (5'-(*CP*AP*AP*CP*CP*GP*CP*AP*AP*C)-3')


Mass: 2982.984 Da / Num. of mol.: 2 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 56.8 % / Description: ON HOLD
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1300 mM1dropNaCl
220 mMMES1drop
35 mMdithiothreitol1drop
41 mMEDTA1drop
550 mMHEPES1reservoir
63 %(w/v)PEG80001reservoir
75 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9366
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 2000 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9366 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 27926 / % possible obs: 99.1 % / Redundancy: 6 % / Biso Wilson estimate: 60.1 Å2 / Rsym value: 0.126 / Net I/σ(I): 19.4
Reflection shellResolution: 2.6→2.64 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.38 / % possible all: 98.8
Reflection
*PLUS
Num. measured all: 193723 / Rmerge(I) obs: 0.126
Reflection shell
*PLUS
% possible obs: 98.8 % / Rmerge(I) obs: 0.38

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E50

1e50


Resolution: 2.6→48.02 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1104447.41 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2272 8.1 %RANDOM
Rwork0.237 ---
obs0.237 27926 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.3898 Å2 / ksol: 0.380588 e/Å3
Displacement parametersBiso mean: 48.6 Å2
Baniso -1Baniso -2Baniso -3
1-8.93 Å20 Å20 Å2
2--8.93 Å20 Å2
3----17.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.6→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4003 808 0 56 4867
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.54
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.407 367 8.1 %
Rwork0.36 4174 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3WATER_REP.PARAM&_1_TOPOLOGY_INFILE_3
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.54
LS refinement shell
*PLUS
Rfactor Rwork: 0.36

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